RnoINT0127074 @ rn6
Intron Retention
Gene
ENSRNOG00000054901 | Rif1
Description
replication timing regulatory factor 1 [Source:RGD Symbol;Acc:1562474]
Coordinates
chr3:37629923-37631582:+
Coord C1 exon
chr3:37629923-37629965
Coord A exon
chr3:37629966-37631379
Coord C2 exon
chr3:37631380-37631582
Length
1414 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TCCCCCACTCTTTTTCCTAGTTA
3' ss Score
6.47
Exon sequences
Seq C1 exon
GCTTGATGAGGTTCCTAAAGTGTATACTAGTTTGAACAACAAG
Seq A exon
GTAAGTGGACAGTGTCTATAAAGTAGACCTTATCAATGAGGACAGGGTATGGTTTAGGCAGTAATCTTTGTATACATTATATTATTGTTGCTTTACACTTATATTTGCTGTGTGTGCATATACATATAGTGTCAGACATCAGAGCACTTGTGCAGGATTGGTTCTCTCTTACCACGTAGGTCCCAGGGACTGAAATACCTTCTCTCCTTGCTGTTGATGTAAAAATATAAAAAATAAAAAATGTTGATGTAAAAATATAAAAAATATAAAAGGTATAGTTGTCTTTTTCCCCGCTAGGTCCCCGAGGTGCCCCAAGATATCTGCTAGATATTTTGGCAGAAACACATCCCAACTCTGTGGCGGCCCAGTGTCTCTTGCCACCACACCCTTTCCTACACTCAAACCGTCACATAAAAGAACACACAACACAATAACCTTTGACCCAAATGGTAAGATATAATTGCCCACTTAAACATACAAAGCCTGGTACTATCCCTCCCTTAGGAACATATAATAACAATTGTAAATACACAGAGCAGAATCTTAACATCACCTGCCATGGCTTCTCACCCTCTCCTCTGTCCTGTCTCCTTTCTCCTCTAGTCTCCTCTTCCTTCAAACTTCTCTCTTGCCCATCCTTCCTTCTCCAATGACAGTCCTCCTTCTATCCTGTACCTGCCCTTCACCTGTACTTTACAAATTCAATGGGGAGGTGGTTCTGGTGAAGTTACCTGAGTTCTGAGTACCTGACTAGGCAATTGTCCTTGGGGCAGTGGAATTAGCATCAAAATAAAATAACTTCAGGGCAAACTACAACACTTTGCCATCTTACTTCATTTTAAAAAATTCTTTTTTCTTTAAAAAAAATGTATGCATGTGTGTATAATTGTCCATAAATATATTCACCATGGAGGTCAGAAGAAGGTCCAGTGGAGCTATAGTCATAGGCAGGTCAGGGACTGAGAACTGAACTGTCTTCTGGAAGCAAGTTGCAAGTGTTGGCTATCCACTGAATCCTCCCAGCCCCATTGCTTCATTTTTAGGGGACATAAAATAATGGGGTTTAGATGCATTCTTAAGTAGCTGGGTTTACTTTAAATTCATGTAATTTCTCAGGTCTCATCTCTTTTTATATGAGATTGTGGGCGGTAATATATTAATTGTACAGATGATTATTAATCACTGTTGCAATTAATAAGAAACCTTTTTCTGTTCACAAGAAAGAGCTGTGAATCAAGTTACAGCACTAATACTAAGTAAATTTACCTGATAGCTTGTTCATATGTAAAAAGGATGACATATTTATGATGACCATGGTGTTGCTTAAAGATGTTCCGGATTTTAATGGAAATAGTAACATATTCCACAAATTTGTATTTACAATACCTTTTGTTTCCCCCACTCTTTTTCCTAG
Seq C2 exon
TTAGAAAAGTTATTAGGAGAAATTGTTGCTTGTCTACAGTTCAACTATCTTGGAGCCTATGACAGTGAACTTCTTGGACAACTTTCTCCACTCCTGTGCATAATTTTTCTTCACAAGAATAAACAGATTCGGAAACAGAGTGCTGTGTTGTGGAATGCTACATTTGCTAAAGCAACAGCTCTGATCTATCCTGAGGAATTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000054901:ENSRNOT00000090575:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTGATGAGGTTCCTAAAGTGT
R:
TTTAATTCCTCAGGATAGATCAGAGC
Band lengths:
246-1660
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]